Re^2: Aligning protein sequences using MUSCLE through Perl

i changed my code and downloaded your fasta to make a check but i get this annoying message :

'-in' not recognized as an internal or external command,
executable program or script file.

--------------------- WARNING ---------------------
MSG: Muscle call crashed: 256 [command  -in sequence.fa  -out outfile.
+fa]

---------------------------------------------------
[download]

any more clue??? really thanks for your help!

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Re^3: Aligning protein sequences using MUSCLE through Perl by Anonymous Monk on Mar 14, 2015 at 17:05 UTC
So your version of muscle is called "-in"? See https://metacpan.org/pod/Bio::Tools::Run::Alignment::Muscle#Helping-the-module-find-your-executable	[reply]